Archimesh: Undoing bad topology with the walls: How?
If you want to edit freely with archimesh objects, you'd have to convert them to meshes (select your object then click object > convert to > mesh from curve/meta/surf/text) but it may compromise your archimesh tools with more complex models. Archimesh objects don't give you freedom in edit mode and most edits affect the whole mesh and/or aren't flexible at all, so I personally found that converting objects to a mesh and making most doors from scratch was a lot better for me because I prefer more freedom and flexibility. 

And for the auto holes to work properly in general, the doors/windows need to be thinner than the walls which makes sense but also takes some time playing around with. And the minute you make even the slightest change, the hole disappears and you have to check "Auto holes" again and again. 

If you want to create your own doors/holes with the same archimesh walls without converting it to a mesh, the Bisect tool works best. Loops and knife cuts cause too much complication with archimesh objects due to the lack of freedom so Bisect tool is your best choice.